PNNL

Dr. Katrina Waters is a Laboratory Fellow and Chief Scientist for biological sciences research at the Pacific Northwest National Laboratory (PNNL). Her research interests are focused at the intersection of environmental exposures and infectious disease on human health. With more than 150 publications, she has built a national and international reputation through her leadership and innovation in data integration and interpretation for systems toxicology data as well as high-throughput screening data. Her programs include the study of health effects of chemicals at Superfund sites and personal environmental exposure assessment for epidemiological studies in disadvantaged communities. She is currently Deputy Director of the Oregon State University (OSU) – PNNL Superfund Research Center. Recently, she completed a Department of Energy research program focused on airborne and environmental transmission of COVID-19.  She has also led numerous research efforts in computational modeling, bioinformatics, and data management for a National Institute of Allergy and Infectious Diseases (NIAID) Center for Predictive Modeling of Infectious Diseases and a Department of Homeland Security program for Predictive Modeling of Viral Infections. Dr. Waters holds joint faculty appointments with OSU and the University of Washington.

• Pathway-based biomarker discovery for environmental exposure to toxicants, including disease susceptibility factors
• High-throughput screening approaches for hazard assessment and mechanism-based risk assessment
• Predictive modeling of lethal human viral infections, including influenza, SARS, Ebola, and West Nile virus
• Development of computational tools for integration of genomics, proteomics, metabolomics, and high-throughput data

• Postdoctoral Fellowship with Kevin Gaido, Chemical Industry Institute of Toxicology Centers for Health Research, Research Triangle Park
• National Research Service Award Postdoctoral Fellowship with Thomas C. Spelsberg, Mayo Graduate School of Medicine
• PhD in Biochemistry, University of Wisconsin
• AB in Chemistry, Ripon College

• Full Member, Society of Toxicology (SOT) (2009-present)
• Member and Chair, Environmental Protection Agency’s (EPA) Board of Scientific Counselors Subcommittee on Chemical Safety for Sustainability (2018-2020)
• Science Advisory Board, National Toxicology Program of NIEHS for the Secretary of Health and Human Services (2016-2019)
• Scientific Advisory Board, Center for Genome Research and Biocomputing, OSU (2013-2018)
• Member, Endocrine-Related Low Dose Toxicity Committee, National Academy of Science (NAS), evaluated EPA’s current regulatory toxicity testing strategy for low dose exposures (2015-2017)
• Member, EPA’s Board of Scientific Counselors Subcommittee on Chemical Safety for Sustainability (2014-2017)
• Member, Scientific Advisory Board, Food and Drug Administration National Center for Toxicological Research (2013-2016)
• Member, NAS Committee on Predictive Toxicology Approaches for Military Assessments of Acute Exposures (2014-2015)
• PNNL Representative, Department of Energy Ebola Task Force, participated in Biomedical Advanced Research and Development Authority Modeling meetings (2014-2015)
• Member, Scientific Advisory Panel on Methods for Prioritizing Endocrine Disrupting Chemicals using Computational Toxicology Tools, EPA (2013)
• Board of Scientific Counselors, EPA Subcommittee for Computational Toxicology (2009-2012)
• Editorial Board, Toxicology and Applied Pharmacology (2008-2012)
• Associate Member, Society for Toxicologic Pathology (2006-2011)
• Journal Reviews: Frontiers in Big Data (associate editor), Endocrinology, Journal of Bone and Mineral Research, Toxicological Sciences, Environmental Health Perspectives, Journal of Toxicologic Pathology, Toxicology and Applied Pharmacology (past associate editor), BMC Systems Biology, PLOS Computational Biology.

• Election as Fellow of the American Association for the Advancement of Science (2023)
• Election to the Washington State Academy of Sciences, Section 3 Biological Sciences (2021)

• Secretary of Energy Appreciation Award for the National Virtual Biotechnology Laboratory mobilizing the scientific facility and research capabilities of the DOE National Laboratories for COVID (2021)

• Laboratory Fellow, PNNL, the highest level of scientific achievement for program development, international recognition, and scientific accomplishment (2018)
• Secretary of Energy Appreciation Award for the National Laboratory Ebola Task Force Team, Department of Energy (2017)
• James and Mildred Oldfield/E.R. Jackman Team Award, OSU/PNNL Superfund Research Program: “PAHs: New Technologies and Emerging Health Threats,” OSU (2015)
• Best Presentation in Mixtures, SOT Mixtures Specialty Section (2012)
• Outstanding Poster Travel Award, Gordon Conference on Toxicogenomics (2007)
• Outstanding Performance Award, PNNL (2006)
• Plenary Poster Award, American Society for Bone and Mineral Research (1998)
• National Research Service Award, National Cancer Institute Postdoctoral Fellowship (1997-1999)

http://www.ncbi.nlm.nih.gov/myncbi/browse/collection/44773835/?sort=date&direction=ascending

PNNL Publications

2024

• Colvin V., L.M. Bramer, B.N. Rivera, J. Pennington, K.M. Waters, and S.C. Tilton. 2024. Modeling PAH mixture interactions in a human in vitro 3D respiratory culture system. International Journal of Molecular Sciences, 25(8), 4326. https://doi.org/10.3390/ijms25084326.
• Eisfeld A.J., L.N Anderson, S. Fan, K.B. Walters, P.J. Halfmann, D. Westhoff Smith, L.B. Thackray, Q. Tan, A.C. Sims, V.D. Menachery, A. Schäfer, T.P. Sheahan, A.S. Cockrell, K.G. Stratton, B.M. Webb-Robertson, J.E. Kyle, K.E. Burnum-Johnson, Y.M. Kim, C.D. Nicora, Z. Peralta, A.U. N'jai, F. Sahr, H. van Bakel, M.S. Diamond, R.S. Baric, T.O. Metz, R.D. Smith, Y. Kawaoka, and K.M. Waters. 2024. A compendium of multi-omics data illuminating host responses to lethal human virus infections. Scientific Data, 11(1):328. https://doi.org/10.1038/s41597-024-03124-3. 
• Bramer L.M., H.M. Dixon, D. Rohlman, R.P. Scott, R.L. Miller, L. Kincl, J.B. Herbstman, K.M. Waters, and K.A. Anderson. 2024. PM2.5 is insufficient to explain personal PAH exposure. Geohealth 8(2): e2023GH000937.  https://doi.org/10.1029/2023GH000937. 
• McLarnan SM, LM Bramer, HM Dixon, RP Scott, LP Calero, D Holmes, EA Gibson, HM Cavalier, D Rohlman, RL Miller, L Kincl, KM Waters, K.A. Anderson and J.B. Herbstman. 2024. Predicting Personal PAH Exposure using High Dimensional Questionnaire and Wristband Data. J Expo Sci Environ Epidemiol. 2024 Jan 5. https://doi.org/10.1038/s41370-023-00617-y.  
• Bramer L.M., H.M. Dixon, D.J. Degnan, D. Rohlman, J.B. Herbstman, K.A. Anderson, and K.M. Waters. 2024. Expanding the access of wearable silicone wristbands in community-engaged research through best practices in data analysis and integration. Pacific Symposium on Biocomputing, 29, 170-186. https://doi.org/10.1142/9789811286421_0014. 

2023

• Riley K.W., K. Burke, A. Cole, M. Ureno, H.M. Dixon, L. Calero, L.M. Bramer, K.M. Waters, K.A. Anderson, J.B. Herbstman, and D. Rohlman. 2023. Factors that Influence Environmental Health Literacy from Returning Polycyclic Aromatic Hydrocarbon Exposure Results. International Public Health Journal. 15(3), pp.317-331.
• McClure R.S., Y. Rericha, K.M. Waters, and R.L. Tanguay. 2023. 3’ RNA-seq is superior to standard RNA-seq in cases of sparse data but inferior identifying toxicity pathways in a model organism. Frontiers in Bioinformatics, 3:1234218. https://doi.org/10.3389/fbinf.2023.1234218. 
• Fritch E.J., W. Sanders, A.C. Sims, L. Herring, N.K. Barker, A.A. Schepmoes, K.K. Weitz, J.R. Texier, D. Dittmer, L.M. Graves, R.D. Smith, K.M. Waters, N.J. Moorman, R. Baric and R.L. Graham. 2023. Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East Respiratory Syndrome Coronavirus infection. iScience, 26(6):106780. https://doi.org/10.1016/j.isci.2023.106780. 
• Gosline S., D.N. Kim, P. Pande, D.G. Thomas, L. Truong, P. Hoffman, M. Barton, J.P. Loftus, S.D. Hampton, S.T. Dowson, L. Franklin, D.J. Degnan, L.N. Anderson, R.L. Tanguay, K.A. Anderson, and K.M. Waters. 2023. The Superfund Research Program Analytics Portal: linking environmental chemical exposure to biological phenotypes. Scientific Data, 10(1):151. https://doi.org/10.1038/s41597-023-02021-5. 
• Bramer, L.M., R.D. Hontz, A.J. Eisfeld, A.C. Sims, Y.M. Kim, K.G. Stratton, C.D. Nicora, M.A. Gritsenko, A.A. Schepmoes, O. Akasaka, M. Koga, T. Tsutsumi, M. Nakamura, I. Nakachi, R. Baba, H. Tateno, S. Suzuki, H. Nakajima, H. Kato, K. Ishida, M. Ishii, Y. Uwamino, K. Mitamura, V.L. Paurus, E.S. Nakayasu, I.K. Attah, A.G. Letizia, K.M. Waters, T.O. Metz, K. Corson, Y. Kawaoka, and V.R. Gerbasi. 2023. Multi-omics of NET formation and correlations with CNDP1, PSPB, and L-cystine levels in severe and mild COVID-19 infections. Heliyon, 9(3):e13795. https://doi.org/10.1016/j.heliyon.2023.e13795. 
• Rude C.I., L.G. Tidwell, S.C. Tilton, K.M. Waters, K.A. Anderson, and R.L. Tanguay. 2023. Coupling environmental whole mixture toxicity screening with unbiased RNAseq reveals site-specific biological responses in zebrafish. Toxics, 11(3):201. https://doi.org/10.3390/toxics11030201. 
• Flores J.E., D.M. Claborne, Z. Weller, B.M. Webb-Robertson, K.M. Waters, and L.M. Bramer. 2023. Missing Data in Multi-Omics Integration: Recent Advances Through Artificial Intelligence. Frontiers in Artificial Intelligence, 6:1098308.https://doi.org/10.3389/frai.2023.1098308. 

2022

• Wilson, L.B., R.S. McClure, K.M. Waters, M. Simonich, and R.L. Tanguay. 2022. Concentration-response gene expression analysis in zebrafish reveals phenotypically-anchored transcriptional responses to retene. Frontiers in Toxicology, 4:950503. https://doi.org/10.3389/ftox.2022.950503. 
• Evoy R., L. Kincl, D. Rohlman, L.M. Bramer, H.M. Dixon, P. Hystad, H. Bae, M. Barton, A.R. Phillips, R. Miller, K.M. Waters, J.B. Herbstman, and K.A. Anderson. 2022. Impact of acute temperature and air pollution exposures on adult lung function: a study of asthmatics. PLOS One, 17(6):e0270412. https://doi.org/10.1371/journal.pone.0270412. 
• Shankar P., G.R. Garcia, J.K. La Du, C.M. Sullivan, C.L. Dunham, B.C. Goodale, K.M. Waters, S. Stanisheuski, C.S. Maier, P. Thunga, D.M. Reif, R.L. Tanguay. 2022. The Ahr2-dependent wfikkn1 gene influences zebrafish transcriptome, proteome and behavior. Toxicological Sciences, 187(2):325-344. https://doi.org/10.1093/toxsci/kfac037. 
• Dixon H.M., L.M. Bramer, R.P. Scott, L.P. Calero, D. Holmes, E.A. Gibson, H.M. Cavalier, D. Rohlman, R.L. Miller, A. Calafat, L. Kincl, K.M. Waters, J.B. Herbstman and K.A. Anderson. 2022. Evaluating predictive relationships between wristbands and urine for assessment of personal PAH exposure. Environment International, 163:107226.https://doi.org/10.1016/j.envint.2022.107226. 

2021

• Feng S., E. Heath, B.A. Jefferson, C.A. Joslyn, H.J. Kvinge, H.D. Mitchell, and B.L. Praggastis, et al. 2021. "Hypergraph Models of Biological Networks to Identify Genes Critical to Pathogenic Viral Response." BMC Bioinformatics 22, no. 1:287. PNNL-SA-155930. doi:10.1186/s12859-021-04197-2
• Kyle J.E., K.G. Stratton, E.M. Zink, Y. Kim, K.J. Bloodsworth, M.E. Monroe, and K.M. Waters, et al. 2021. "A resource of lipidomics and metabolomics data from individuals with undiagnosed diseases." Scientific Data 8, no. 1:114. PNNL-SA-150181. doi:10.1038/s41597-021-00894-y
• Mansouri K., A. Karmaus, J. Fitzpatrick, G. Patlewicz, P. Pradeep, D. Alberga, and N. Alepee, et al. 2021. "CATMoS: Collaborative Acute Toxicity Modeling Suite." Environmental Health Perspectives 129, no. 4:047013. PNNL-SA-159448. doi:10.1289/EHP8495
• O'Callahan B.T., O. Qafoku, V. Balema, O. Negrette, A. Passian, M.H. Engelhard, and K.M. Waters. 2021. "Atomic force microscopy and infrared nanospectroscopy of COVID-19 spike protein for quantification of adhesion to common surfaces." Langmuir 37, no. 41:12089-12097. PNNL-SA-164328. doi:10.1021/acs.langmuir.1c01910
• Shankar P., R.S. McClure, K.M. Waters, and R.L. Tanguay. 2021. "Gene Co-Expression Network Analysis in Zebrafish Reveals Chemical Class Specific Modules." BMC Genomics 22, no. 1:658. PNNL-SA-160902. doi:10.1186/s12864-021-07940-4
• Sims A.C., H.D. Mitchell, L. Gralinski, J.E. Kyle, K.E. Burnum-Johnson, M. Lam, and L.M. Fulcher, et al. 2021. "Unfolded Protein Response Inhibition Reduces Middle East Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 12, no. 4:e01572-21. PNNL-SA-162254. doi:10.1128/mBio.01572-21

2020

• Webb-Robertson BM, KG Stratton, JE Kyle, Y Kim, KM Waters, D Koeller, and TO Metz. 2020. "Statistically-driven Metabolite and Lipid Profiling of Patients from the Undiagnosed Diseases Network." Analytical Chemistry, 2020 Jan 21;92(2):1796-1803. doi: 10.1021/acs.analchem.9b03522. PMID: 31742994.
• Truong L., S.W. Marvel, D. Reif, D. Thomas, P. Pande, S. Dasgupta, and M. Simonich, et al. 2020. "The multi-dimensional embryonic zebrafish platform predicts flame retardant bioactivity." Reproductive Toxicology 96. PNNL-SA-149984. doi:10.1016/j.reprotox.2020.08.007

2019

• Bramer L.M., K.G. Stratton, A.M. White, A.A. Bleeker, M.A. Kobold, K.M. Waters, and T.O. Metz, et al. 2019. "P-Mart: Interactive Analysis of Ion Abundance Global Proteomics Data." Journal of Proteome Research 18, no. 3:1426-1432. PNNL-SA-140572. doi:10.1021/acs.jproteome.8b00840
• Brown J.M., A.R. Phillips, D.A. Lewis, M. Mans, Y. Chang, R. Tanguay, and E.S. Peterson, et al. 2019. "Bioinformatics Resource Manager: A systems biology web tool for microRNA and omics data integration." BMC Bioinformatics 20:Article No. 255. PNNL-SA-138423. doi:10.1186/s12859-019-2805-6
• Burnum-Johnson K.E., X. Zheng, J.N. Dodds, J. Ash, D. Fourches, C.D. Nicora, and J.P. Wendler, et al. 2019. "Ion mobility spectrometry and the omics: Distinguishing isomers, molecular classes and contaminant ions in complex samples." TrAC Trends in Analytical Chemistry 116:292-299. PNNL-SA-140985. doi:10.1016/j.trac.2019.04.022
• Dixon H.M., G. Armstrong, M. Barton, A.J. Bergmann, M. Bondy, M.L. Halbleib, and W. Hamilton, et al. 2019. "Discovery of common chemical exposures across three continents using silicone wristbands." Royal Society Open Science 6, no. 2:181836. PNNL-SA-139109. doi:10.1098/rsos.181836
• Madeen E.P., L.E. Siddens, S. Uesugi, T.J. McQuistan, R.A. Corley, J.N. Smith, and K.M. Waters, et al. 2019. "Toxicokinetics of Benzo[a]pyrene in Humans: Extensive Metabolism as Determined by UPLC-Accelerator Mass Spectrometry Following Oral Micro-Dosing." Toxicology and Applied Pharmacology 364:97-105. PNNL-SA-132492. doi:10.1016/j.taap.2018.12.010
• McClure R.S., J.P. Wendler, J.N. Adkins, J.A. Swanstrom, R. Baric, B. Kaiser, and K.L. Oxford, et al. 2019. "Unified Feature Association Networks through Integration of Transcriptomic and Proteomic Data." PLoS Computational Biology 15, no. 9:e1007241. PNNL-SA-137420. doi:10.1371/journal.pcbi.1007241
• Messier K.P., L.G. Tidwell, C. Ghetu, D. Rohlman, R.P. Scott, L.M. Bramer, and H.M. Dixon, et al. 2019. "Indoor versus Outdoor Air Quality During Wildfires." Environmental Science & Technology Letters 6, no. 12:696-701. PNNL-SA-147722. doi:10.1021/acs.estlett.9b00599
• Mitchell H.D., A.J. Eisfeld, K.G. Stratton, N.C. Heller, L.M. Bramer, J. Wen, and J.E. McDermott, et al. 2019. "The Role of EGFR in Influenza Pathogenicity: Multiple Network-based Approaches To Identify a Key Regulator of Non-Lethal Infections." Frontiers in Cell and Developmental Biology 7:Article No. 200. PNNL-SA-142083. doi:10.3389/fcell.2019.00200
• Rohlman D., H.M. Dixon, L. Kincl, A.J. Larkin, R. Evoy, M. Barton, and A.R. Phillips, et al. 2019. "Development of an Environmental Health Tool Linking Chemical Exposures, Physical Location and Lung Function." BMC Public Health 19:854. PNNL-SA-138638. doi:10.1186/s12889-019-7217-z
• Shankar P., M. Geier, L. Truong, R.S. McClure, P. Pande, K.M. Waters, and R. Tanguay. 2019. "Coupling Genome-wide Transcriptomics and Developmental Toxicity Profiles in Zebrafish to Characterize Polycyclic Aromatic Hydrocarbon (PAH) Hazard." International Journal of Molecular Sciences 20, no. 10:2570. PNNL-SA-143672. doi:10.3390/ijms20102570
• Stratton K.G., B.M. Webb-Robertson, L. McCue, B.A. Stanfill, D.M. Claborne, I.G. Godinez, and T. Johansen, et al. 2019. "pmartR: Quality Control and Statistics for Mass Spectrometry-based Biological Data." Journal of Proteome Research 18, no. 3:1418-1425. PNNL-SA-138429. doi:10.1021/acs.jproteome.8b00760
• Kyle JE, KE Burnum-Johnson, JP Wendler, AJ Eisfeld, PJ Halfmann, T Watanabe, F Sahr, RD Smith, Y Kawaoka, KM Waters, and TO Metz. 2019. "The plasma lipidome reveals critical illness and disease and recovery from human Ebola virus disease." Proc Natl Acad Sci U S A, 116(9):3919-3928. DOI: 10.1073/pnas.1815356116. PMCID: PMC6397561.
• Thomas DG, H Shankaran, L Truong, R Tanguay, and KM Waters. 2019.  "Time-dependent behavioral data from embryonic zebrafish reveals novel signatures of chemical toxicity using point of departure analysis."  Journal of Computational Toxicology, 9:50-60. DOI: 10.1016/j.comtox.2018.11.001.  PMCID: PMC6726397

2018

• Dixon H.M., R.P. Scott, D. Holmes, L.P. Calero, L. Kincl, K.M. Waters, and D.E. Camann, et al. 2018. "Silicone wristbands compared with traditional polycyclic aromatic hydrocarbon exposure assessment methods." Analytical and Bioanalytical Chemistry 410, no. 13:3059-3071. PNNL-SA-123134. doi:10.1007/s00216-018-0992-z
• Dorman D.C., W. Chiu, B.F. Hales, R. Hauser, K.J. Johnson, E. Mantus, and S. Martel, et al. 2018. "Polybrominated Diphenyl Ether (PBDE) Neurotoxicity: A Systematic Review and Meta-Analysis of Animal Evidence." Journal of Toxicology and Environmental Health Part B 21, no. 4:269-289. PNNL-SA-130979. doi:10.1080/10937404.2018.1514829
• Dorman D.C., W. Chiu, B.F. Hales, R. Hauser, K.J. Johnson, E. Mantus, and S. Martel, et al. 2018. "Systematic Reviews and Meta-analyses of Human and Animal Evidence of Prenatal Diethylhexyl Phthalate Exposure and Changes in Male Anogenital Distance." Journal of Toxicology and Environmental Health Part B 21, no. 4:207-226. PNNL-SA-130356. doi:10.1080/10937404.2018.1505354
• Haggard D.E., P.D. Noyes, K.M. Waters, and R. Tanguay. 2018. "Transcriptomic and phenotypic profiling in developing zebrafish exposed to thyroid hormone receptor agonists." Reproductive Toxicology 77:80-93. PNNL-SA-122324. doi:10.1016/j.reprotox.2018.02.006
• Menachery V.D., A. Schafer, K.E. Burnum-Johnson, H.D. Mitchell, A.J. Eisfeld-Fenney, K.B. Walters, and C.D. Nicora, et al. 2018. "MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape." Proceedings of the National Academy of Sciences of the United States of America 115, no. 5:E1012-E1021. PNNL-SA-126254. doi:10.1073/pnas.1706928115
• Menachery V.D., L. Gralinski, H.D. Mitchell, K. Dinnon, Iii, S.R. Leist, B. Yount, and E. Mcanarney, et al. 2018. "Combination attenuation offers strategy for live-attenuated coronavirus vaccines." Journal of Virology 92, no. 17:e00710-18. PNNL-SA-134212. doi:10.1128/JVI.00710-18
• Oláhová M, WH Yoon, K Thompson, S Jangam, LF Betancourt, JM Davidson, JE Kyle, ME Grove, DG Fisk, MJ Holmes, AM Dries, Y Huang, C Zhao, K Contrepois, Z Zappala, L Fresard, D Waggott, EM Zink, YM Kim, HM Heyman, KG Stratton, BM Webb-Robertson, M Snyder, JD Merker, SR Beck-Montgomery, PG Fisher, RG Feichtinger, JA Mayr, J Hall, IA Barbosa, MA Simpson, C Deshpande, KM Waters, D Koeller, TO Metz, A Morris, RD Mcfarland, S Schelley, LL Van Hove, G Enns, S Yamamoto, EA Ashley, ME Wangler, RW Taylor, HJ Bellen, J Bernstein, and M Wheeler.  2018.  "Bi-allelic Mutations in ATP5D, a Subunit of ATP Synthase, Cause a Metabolic Disorder." American Journal of Human Genetics, 2018 Feb 16. pii: S0002-9297(18)30042-9. doi: 10.1016/j.ajhg.2018.01.020.PMCID: PMC6117612.

2017

• Eisfeld AJ, P Halfmann, JP Wendler, JE Kyle, KE Burnum-Johnson, Z Peralta, T Maemura, KB Walters, T Watanabe, S Fukuyama, M Yamashita, JM Jacobs, YM Kim, CP Casey, KG Stratton, BJM Webb-Robertson, MA Gritsenko, ME Monroe, KK Weitz, AK Shukla, M Tian, G Neumann, JL Reed, H Bakel, TO Metz, RD Smith, KM Waters, A N'jai, F Sahr, and Y Kawaoka.  2017.  "Human Ebola Virus Disease Pathogenesis Revealed by Multi-Platform ‘Omics Analysis."  Cell Host and Microbe, 22 (6), 817-829. PMCID: PMC5730472.
• Menachery VD, Gralinski L, Mitchell HD, Leist SR, Yount B, Graham RL, Mcanarney E, Stratton K G, Debbink K, Waters KM, and R Baric.  2017.  "MERS-CoV NSP16 necessary for IFN resistance and viral pathogenesis" mSphere 2017 Nov 15;2(6). pii: e00346-17. doi: 10.1128/mSphere.00346-17. PMCID: PMC5687918

• Burnum-Johnson K.E., J.E. Kyle, A.J. Eisfeld, C.P. Casey, K.G. Stratton, J.F. Gonzalez, and F. Habyarimana, et al. 2017. "MPLEx: A method for simultaneous pathogen inactivation and extraction of samples for multi-omics profiling." Analyst 142, no. 3:442-448. PNNL-SA-116063. doi:10.1039/c6an02486f
• Davie-Martin C.L., K.G. Stratton, J.G. Teeguarden, K.M. Waters, and S.L. Massey Simonich. 2017. "Implications of bioremediation of polycyclic aromatic hydrocarbon-contaminated soils for human health and cancer risk." Environmental Science & Technology 51, no. 17:9458-9468. PNNL-SA-122323. doi:10.1021/acs.est.7b02956
• Madeen E.P., C.V. Lohr, H. You, L.E. Siddens, S.K. Krueger, R.H. Dashwood, and F.J. Gonzalez, et al. 2017. "Dibenzo[def,p]chrysene transplacental carcinogenesis in wild-type, Cyp1b1 knockout, and CYP1B1 humanized mice." Molecular Carcinogenesis 56, no. 1:163-171. PNWD-SA-10523. doi:10.1002/mc.22480
• Menachery V.D., H.D. Mitchell, A. Cockrell, L. Gralinski, B. Yount, R.L. Graham, and E. Mcanarney, et al. 2017. "MERS-CoV Accessory ORFs play key role for infection and pathogenesis." mBio 8, no. 4:Article No. e00665-17. PNNL-SA-126255. doi:10.1128/mBio.00665-17
• Menachery V.D., L. Gralinski, H.D. Mitchell, K. Dinnon, Iii, S.R. Leist, B. Yount, and R.L. Graham, et al. 2017. "Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 is Necessary for Interferon Resistance and Viral Pathogenesis." mSphere 2, no. 6:Article No. e00346-17. PNNL-SA-128149. doi:10.1128/mSphere.00346-17
• Powell J.D., and K.M. Waters. 2017. "Influenza-omics and the host response: recent advances and future prospects." Pathogens 6, no. 2:25. PNNL-SA-126286. doi:10.3390/pathogens6020025
• Co-author of NAS committee report, published July 18, 2017:  National Academies of Sciences, Engineering, and Medicine. 2017. “Application of Systematic Review Methods in an Overall Strategy for Evaluating Low-Dose Toxicity from Endocrine Active Chemicals.” Washington, DC: The National Academies Press. https://doi.org/10.17226/24758.
• Webb-Robertson BJM, TO Metz, KM Waters, Q Zhang, M Rewers. (2017) “Bayesian Posterior Integration for Classification of Mass Spectrometry Data.” In: Datta S., Mertens B. (eds) Statistical
• Analysis of Proteomics, Metabolomics, and Lipidomics Data Using Mass Spectrometry. Frontiers in Probability and the Statistical Sciences. Springer, Cham.  doi:10.1007/978-3-319-45809-0_11
• Wittwehr C, H Aladjov, GT Ankley, HJ Byrne, J de Knecht, E Heinzle, G Klambauer, B Landesmann, M Luijten, C MacKay, G Maxwell, B Meek, A Paini, E Perkins, T Sobanski, KM Waters, and M Whelan.  2017.  "How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology." Toxicological Sciences, 155(2): 326-336. doi: 10.1093/toxsci/kfw207. PMCID: PMC5340205.

2016

• Haggard D.E., P.D. Noyes, K.M. Waters, and R. Tanguay. 2016. "Phenotypically anchored transcriptome profiling of developmental exposure to the antimicrobial agent, triclosan, reveals hepatotoxicity in embryonic zebrafish." Toxicology and Applied Pharmacology 308:32-45. PNWD-SA-10549. doi:10.1016/j.taap.2016.08.013
• McDermott J.E., H.D. Mitchell, L. Gralinski, A.J. Eisfeld, L. Josset, A. Bankhead, and G. Neumann, et al. 2016. "The Effect of inhibition of PP1 and TNFa signaling on pathogenesis of SARS coronavirus." BMC Systems Biology 10, no. 1:93. PNNL-SA-118784. doi:10.1186/s12918-016-0336-6
• Oxford K.L., J.P. Wendler, J.E. McDermott, R.A. White, J.D. Powell, J.M. Jacobs, and J.N. Adkins, et al. 2016. "The Landscape of Viral Proteomics and Its Potential to Impact Human Health." Expert Review of Proteomics 13, no. 6:579-591. PNNL-SA-116259. doi:10.1080/14789450.2016.1184091
• Teeguarden J.G., Y. Tan, S. Edwards, J.A. Leonard, K. Anderson, R.A. Corley, and M.L. Kile, et al. 2016. "Expanding on Successful Concepts, Models, and Organization." Environmental Science & Technology 50, no. 17:8921-8922. PNNL-SA-119240. doi:10.1021/acs.est.6b03027
• Teeguarden J.G., Y. Tan, Y. Tan, S. Edwards, J.A. Leonard, K.A. Anderson, and R.A. Corley, et al. 2016. "Completing the Link between Exposure Science and Toxicology for Improved Environmental Health Decision Making: The Aggregate Exposure Pathway Framework." Environmental Science & Technology 50, no. 9:4579-4586. PNNL-SA-114098. doi:10.1021/acs.est.5b05311
• Tisoncik-Go J., D.J. Gasper, J.E. Kyle, A.J. Eisfeld, C. Selinger, M. Hatta, and J. Morrison, et al. 2016. "Integrated Omics Analysis of Pathogenic Host Responses during Pandemic H1N1 Influenza Virus Infection: The Crucial Role of Lipid Metabolism." Cell Host & Microbe 19, no. 2:254-66. PNWD-SA-10483. doi:10.1016/j.chom.2016.01.002
• Wang M., J.J. Carver, V.V. Phelan, L.M. Sanchez, N. Garg, Y. Peng, and D. Nguyen, et al. 2016. "Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking." Nature Biotechnology 34, no. 8:828-837. PNWD-SA-10551. doi:10.1038/nbt.3597
• Wittwehr C., H. Aladjov, G.T. Ankley, H.J. Byrne, J. de Knecht, E. Heinzle, and G. Klambauer, et al. 2016. "How Adverse Outcome Pathways Can Aid the Development and Use of Computational Prediction Models for Regulatory Toxicology." Toxicological Sciences 155, no. 2:326-336. PNNL-SA-117451. doi:10.1093/toxsci/kfw207

2015

• Goodale B., J.K. La Du, S.C. Tilton, C.M. Sullivan, W.H. Bisson, K.M. Waters, and R. Tanguay. 2015. "Ligand-specific transcriptional mechanisms underlie aryl hydrocarbon receptor-mediated developmental toxicity of oxygenated PAHs." Toxicological Sciences 147, no. 2:397-411. PNWD-SA-10474. doi:10.1093/toxsci/kfv139
• Hu J.Z., X. Wang, J. Feng, B.M. Webb-Robertson, K.M. Waters, S.C. Tilton, and J.G. Pounds, et al. 2015. "Metabolite Signatures in Hydrophilic Extracts of Mouse Lungs Exposed to Cigarette Smoke Revealed By 1H NMR Metabolomics Investigation." Metabolomics 5, no. 2:Article No. 143. PNNL-SA-102290. doi:10.4172/2153-0769.1000143
• Kebaabetswe L.P., A.K. Haick, M.A. Gritsenko, T.L. Fillmore, R.K. Chu, S.O. Purvine, and B.M. Webb-Robertson, et al. 2015. "Proteomic Analysis Reveals Down-Regulation of Surfactant Protein B in Murine Type II Pneumocytes Infected with Influenza A Virus." Virology 438:96-107. PNWD-SA-10439. doi:10.1016/j.virol.2015.03.045
• Lafontaine S., J. Schrlau, J. Butler, Y. Jia, B.L. Harper, S.G. Harris, and L.M. Bramer, et al. 2015. "RELATIVE INFLUENCE OF TRANS-PACIFIC AND REGIONAL ATMOSPHERIC TRANSPORT OF PAHS IN THE PACIFIC NORTHWEST, U.S." Environmental Science & Technology 49, no. 23:13807-13816. PNWD-SA-10478. doi:10.1021/acs.est.5b00800
• Lovelace E.S., J. Wagoner, J. MacDonald, T. Bammler, J. Bruckner, J. Brownell, and R. Beyer, et al. 2015. "Silymarin Suppresses Cellular Inflammation By Inducing Reparative Stress Signaling." Journal of Natural Products 78, no. 8:1990-2000. PNNL-SA-109357. doi:10.1021/acs.jnatprod.5b00288
• Rohlman D., L. Syron, K. Hobbie, K. Anderson, C. Scaffidi, D. Sudakin, and E.S. Peterson, et al. 2015. "A Community-Based Approach to Developing a Mobile Device for Measuring Ambient Air Exposure, Location and Respiratory Health." Environmental Justice 8, no. 4:126-134. PNWD-SA-10454. doi:10.1089/env.2015.0001
• Siddens L.K., K.L. Bunde, T.A. Harper Jr., T.J. McQuistan, C.V. Lohr, L.M. Bramer, and K.M. Waters, et al. 2015. "Cytochrome P450 1b1 in Polycyclic Aromatic Hydrocarbon (PAH)-Induced Skin Carcinogenesis: Tumorigenicity of Individual PAHs and Coal-Tar Extract, DNA Adduction and Expression of Select Genes in the Cyp1b1 Knockout Mouse Toxicology and Applied Pharmacology." Toxicology and Applied Pharmacology 287, no. 2:149-160. PNWD-SA-10455. doi:10.1016/j.taap.2015.05.019
• Tilton S.C., L.K. Siddens, S.K. Krueger, A.J. Larkin, C.V. Lohr, D.E. Williams, and W.M. Baird, et al. 2015. "Mechanism-based Classification of PAH Mixtures to Predict Carcinogenic Potential." Toxicological Sciences 146, no. 1:135-45. PNWD-SA-10456. doi:10.1093/toxsci/kfv080
• Tilton S.C., M.M. Matzke, M.B. Sowa, D.L. Stenoien, T.J. Weber, W.F. Morgan, and K.M. Waters. 2015. "Data Integration Reveals Key Homeostatic Mechanisms Following Low Dose Radiation Exposure." Toxicology and Applied Pharmacology 285, no. 2:1-11. PNNL-SA-102570. doi:10.1016/j.taap.2015.01.019
• Webb-Robertson B.M., H.K. Wiberg, M.M. Matzke, J.N. Brown, J. Wang, J.E. McDermott, and R.D. Smith, et al. 2015. "Review, Evaluation, and Discussion of the Challenges of Missing Value Imputation for Mass Spectrometry-Based Label-Free Global Proteomics." Journal of Proteome Research 14, no. 5:1993-2001. PNWD-SA-10158. doi:10.1021/pr501138h

2014

• Aevermann B., B.E. Pickett, S. Kumar, E.B. Klem, S. Agnihothram, P.S. Askovich, and A. Bankhead, et al. 2014. "A Comprehensive Collection of Systems Biology Data Characterizing the Host Response to Viral Infection." Scientific Data 1:Article No. 140033. PNNL-SA-101269. doi:10.1038/sdata.2014.33
• Baulch J.E., U. Aypar, K.M. Waters, A. Yang, and W.F. Morgan. 2014. "Genetic and Epigenetic Changes in Chromosomally Stable and Unstable Progeny of Irradiated Cells." PLoS One 9, no. 9:e107722. PNNL-SA-103002. doi:10.1371/journal.pone.0107722
• Govey P.M., J.M. Jacobs, S.C. Tilton, A.E. Loiselle, Y. Zhang, W.M. Freeman, and K.M. Waters, et al. 2014. "Integrative Transcriptomic and Proteomic Analysis of Osteocytic Cells Exposed to Fluid Flow Reveals Novel Mechano-Sensitive Signaling Pathways." Journal of Biomechanics 47, no. 8:1838-1845. PNWD-SA-10062. doi:10.1016/j.jbiomech.2014.03.022
• Hengel S., J.T. Aldrich, K.M. Waters, L. Pasa-Tolic, and D.L. Stenoien. 2014. "Quantitative Proteomic Profiling of Low Dose Ionizing Radiation Effects in a Human Skin Model." Proteomes 2, no. 3:382-398. PNNL-SA-102010. doi:10.3390/proteomes2030382
• Menachery V., A.J. Eisfeld, A. Schafer, L. Josset, A.C. Sims, S. Proll, and S. Fan, et al. 2014. "Pathogenic Influenza Viruses and Coronaviruses Utilize Similar and Contrasting Approaches to Control Interferon-Stimulated Gene Responses." mBio 5, no. 3:Article No. e01174-14. PNWD-SA-9990. doi:10.1128/mBio.01174-14
• Teeguarden J.G., V.B. Mikheev, K.R. Minard, W.C. Forsythe, W. Wang, G. Sharma, and N.J. Karin, et al. 2014. "Comparative Iron Oxide Nanoparticle Cellular Dosimetry and Response in Mice by the Inhalation and Liquid Cell Culture Exposure Routes." Particle and Fibre Toxicology 11:Article No. 46. PNNL-SA-101188. doi:10.1186/s12989-014-0046-4
• Tilton S.C., N.J. Karin, A. Tolic, Y. Xie, X. Lai, R.F. Hamilton, and K.M. Waters, et al. 2014. "Three Human Cell Types Respond to Multi-Walled Carbon Nanotubes and Titanium Dioxide Nanobelts with Cell-Specific Transcriptomic and Proteomic Expression Patterns." Nanotoxicology 8, no. 5:533-548. PNNL-SA-94058. doi:10.3109/17435390.2013.803624
• Waters K.M., B.S. Cummings, H. Shankaran, N.E. Scholpa, and T.J. Weber. 2014. "ERK Oscillation-Dependent Gene Expression Patterns and Deregulation by Stress-Response." Chemical Research in Toxicology 27, no. 9:1496-1503. PNNL-SA-101628. doi:10.1021/tx500085u
• Webb-Robertson B.M., M.M. Matzke, S. Datta, S.H. Payne, J. Kang, L.M. Bramer, and C.D. Nicora, et al. 2014. "Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements." Molecular and Cellular Proteomics 13, no. 12:3639-3646. PNNL-SA-95335. doi:10.1074/mcp.M113.030932
• Webb-Robertson B.M., Y. Kim, E.M. Zink, K.A. Hallaian, Q. Zhang, R. Madupu, and K.M. Waters, et al. 2014. "A Statistical Analysis of the Effects of Urease Pre-Treatment on the Measurement of the Urinary Metabolome by Gas Chromatography-Mass Spectrometry." Metabolomics 10, no. 5:897-908. PNWD-SA-10204. doi:10.1007/s11306-014-0642-1

2013

• Franzosa J., S. Bugel, T. Tal, J.K. La Du, S.C. Tilton, K.M. Waters, and R. Tanguay. 2013. "Retinoic Acid-Dependent Regulation of miR-19 Expression Elicits Vertebrate Axis Defects." FASEB Journal 27, no. 12:4866-76. PNWD-SA-9975. doi:10.1096/fj.12-225524
• Goodale B., S.C. Tilton, M.M. Corvi, G.V. Wilson, D.B. Janszen, K.A. Anderson, and K.M. Waters, et al. 2013. "Structurally Distinct Polycyclic Aromatic Hydrocarbons Induce Differential Transcriptional Responses in Developing Zebrafish." Toxicology and Applied Pharmacology 272, no. 3:656-670. PNNL-SA-93495. doi:10.1016/j.taap.2013.04.024
• Gralinski L., A. Bankhead, S. Jeng, V. Menachery, S. Proll, S. Belisle, and M.M. Matzke, et al. 2013. "Mechanisms of Severe Acute Respiratory Syndrome Coronavirus-Induced Acute Lung Injury." mBio 4, no. 4:Article No. e00271-13. PNWD-SA-9804. doi:10.1128/mBio.00271-13
• Knecht A., B. Goodale, L. Truong, M. Simonich, A. Swanson, M.M. Matzke, and K.A. Anderson, et al. 2013. "Comparative Developmental Toxicity of Environmentally Relevant Oxygenated PAHs." Toxicology and Applied Pharmacology 271, no. 2:266-275. PNNL-SA-91217. doi:10.1016/j.taap.2013.05.006
• Larkin A.J., L.K. Siddens, S.K. Krueger, S.C. Tilton, K.M. Waters, D.E. Williams, and W.M. Baird. 2013. "Application of a Fuzzy Neural Network Model in Predicting Polycyclic Aromatic Hydrocarbon-Mediated Perturbations of the Cyp1b1 Transcriptional Regulatory Network in Mouse Skin." Toxicology and Applied Pharmacology 267, no. 2:192-199. PNWD-SA-9877. doi:10.1016/j.taap.2012.12.011
• Long J.P., M.S. Kotur, G.V. Stark, R.L. Warren, M.D. Kasoji, J.L. Craft, and R. Albrecht, et al. 2013. "Accumulation of CD11b+GR-1+ Cells in the Lung, Blood and Bone Marrow of Mice Infected with Highly Pathogenic H5N1 and H1N1 Influenza Viruses." Archives of Virology 158, no. 6:1305-22. PNWD-SA-9467. doi:10.1007/s00705-012-1593-3
• Matzke M.M., J.N. Brown, M.A. Gritsenko, T.O. Metz, J.G. Pounds, K.D. Rodland, and A.K. Shukla, et al. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13, no. 3-4:493-503. PNNL-SA-88866. doi:10.1002/pmic.201200269
• Mitchell H.D., A.J. Eisfeld, A. Sims, J.E. McDermott, M.M. Matzke, B.M. Webb-Robertson, and S.C. Tilton, et al. 2013. "A Network Integration Approach to Predict Conserved Regulators Related to Pathogenicity of Influenza and SARS-CoV Respiratory Viruses." PLoS One 8, no. 7:e69374. PNNL-SA-92748. doi:10.1371/journal.pone.0069374
• Motorykin O., M.M. Matzke, K.M. Waters, and S.L. Massey Simonich. 2013. "Association of Carcinogenic Polycyclic Aromatic Hydrocarbon Emissions and Smoking with Lung Cancer Mortality Rates on a Global Scale." Environmental Science & Technology 47, no. 7:3410-3416. PNWD-SA-9831. doi:10.1021/es305295d
• Saili K.S., S.C. Tilton, K.M. Waters, and R. Tanguay. 2013. "Global Gene Expression Analysis Reveals Pathway Differences Between Teratogenic and Non-Teratogenic Exposure Concentrations of Bisphenol A and 17ß-Estradiol in Embryonic Zebrafish." Reproductive Toxicology 38:89-101. PNWD-SA-9894. doi:10.1016/j.reprotox.2013.03.009
• Sims A.C., S.C. Tilton, V. Menachery, L. Gralinski, A. Schafer, M.M. Matzke, and B.M. Webb-Robertson, et al. 2013. "Release of Severe Acute Respiratory Syndrome Coronavirus Nuclear Import Block Enhances Host Transcription in Human Lung Cells." Journal of Virology 87, no. 7:3885-902. PNWD-SA-9741. doi:10.1128/JVI.02520-12
• Tchitchek N., A.J. Eisfeld, J. Tisoncik-Go, L. Josset, L. Gralinski, C. Becavin, and S.C. Tilton, et al. 2013. "Specific Mutations in H5N1 Mainly Impact the Magnitude and Velocity of the Host Response in Mice." BMC Systems Biology 7:Article No. 69. PNNL-SA-94011. doi:10.1186/1752-0509-7-69
• Tilton S.C., K.M. Waters, N.J. Karin, B.M. Webb-Robertson, R.C. Zangar, M.K. Lee, and D.J. Bigelow, et al. 2013. "Diet-Induced Obesity Reprograms the Inflammatory Response of the Murine Lung to Inhaled Endotoxin." Toxicology and Applied Pharmacology 262, no. 2:137-148. PNNL-SA-89403. doi:10.1016/j.taap.2012.12.020
• Tilton S.C., N.J. Karin, B.M. Webb-Robertson, K.M. Waters, V.B. Mikheev, K.M. Lee, and R.A. Corley, et al. 2013. "Impaired Transcriptional Response of the Murine Heart to Cigarette Smoke in the Setting of High Fat Diet and Obesity." Chemical Research in Toxicology 26, no. 7:1034-1042. PNNL-SA-90838. doi:10.1021/tx400078b
• Truong L., S.C. Tilton, T. Zaikovia, E. Richman, K.M. Waters, J.E. Hutchinson, and R. Tanguay. 2013. "Surface Functionalities of Gold Nanoparticles Impact Embryonic Gene Expression Responses." Nanotoxicology 7, no. 2:192-201. PNWD-SA-9547. doi:10.3109/17435390.2011.648225
• Waters K.M., R.L. Sontag, and T.J. Weber. 2013. "Hepatic Leukemia Factor Promotes Resistance To Cell Death: Implications For Therapeutics and Chronotherapy." Toxicology and Applied Pharmacology 268, no. 2:141-148. PNNL-SA-93319. doi:10.1016/j.taap.2013.01.031
• Webb-Robertson B.M., M.M. Matzke, T.O. Metz, J.E. McDermott, J. Walker, K.D. Rodland, and J.G. Pounds, et al. 2013. "Sequential Projection Pursuit Principal Component Analysis - Dealing with Missing Data Associated with New -Omics Technologies." BioTechniques 54, no. 3:165-168. PNNL-SA-87092.
• Waters KM, DL Stenoien, MB Sowa, WB Chrisler, X Wang, R Tan, RL Sontag, and TJ Weber.  2013.  “Annexin A2 Influences Signaling Pathways Induced by Ionizing Radiation through Transcriptional Reprogramming.”  Radiation Research, 179: 53-61. doi: 10.1667/RR3056.1.   

2012

• Chen J., C. Huang, L. Truong, J.K. La Du, S.C. Tilton, K.M. Waters, and K. Lin, et al. 2012. "Early Life Stage Trimethyltin Exposure Induces ADP-Ribosylation Factor Expression and Perturbs the Vascular System in Zebrafish." Toxicology 302, no. 2-3:129-139. PNWD-SA-9327. doi:10.1016/j.tox.2012.09.004
• Diamond D.L., A. Krasnoselski, K.E. Burnum, M.E. Monroe, B.M. Webb-Robertson, J.E. McDermott, and M.M. Yeh, et al. 2012. "Proteome and Computational Analyses Reveal New Insights into the Mechanisms of Hepatitis C Virus Mediated Liver Disease Posttransplantation." Hepatology 56, no. 1:28-38. PNWD-SA-9552. doi:10.1002/hep.25649
• Forsberg N.D., D. Stone, A. Harding, B.L. Harper, S.G. Harris, M.M. Matzke, and A. Cardenas, et al. 2012. "Effect of Native American Fish Smoking Methods on Dietary Exposure to Polycyclic Aromatic Hydrocarbons and Possible Risks to Human Health." Journal of Agricultural and Food Chemistry 60, no. 27:6899-6906. PNWD-SA-9736. doi:10.1021/jf300978m
• Freiin von Neubeck C.H., H. Shankaran, N.J. Karin, P.M. Kauer, W.B. Chrisler, X. Wang, and R.J. Robinson, et al. 2012. "Cell Type-dependent Gene Transcription Profile in Three Dimensional Human Skin Tissue Model Exposed to Low Doses of Ionizing Radiation: Implications for Medical Exposures." Environmental and Molecular Mutagenesis 53, no. 4:247-259. PNNL-SA-79289. doi:10.1002/em.21682
• Goodale B., J.K. La Du, W.H. Bisson, D.B. Janszen, K.M. Waters, and R. Tanguay. 2012. "AHR2 Mutant Reveals Functional Diversity of Aryl Hydrocarbon Receptors in Zebrafish." PLoS One 7, no. 1:e29346. PNWD-SA-9525. doi:10.1371/journal.pone.0029346
• Hobbie K.A., E.S. Peterson, M. Barton, K.M. Waters, and K.A. Anderson. 2012. "Integration of Data Systems and Technology Improves Research and Collaboration for a Superfund Research Center." JALA. Journal of the Association for Laboratory Automation 17, no. 4:275-83. PNWD-SA-9755.
• Matzke M.M., S. Allan, K.A. Anderson, and K.M. Waters. 2012. "An Approach for Calculating a Confidence Interval from a Single Aquatic Sample for Monitoring Hydrophobic Organic Contaminants." Environmental Toxicology and Chemistry 31, no. 12:2888-2892. PNWD-SA-9693. doi:10.1002/etc.2014
• McDermott J.E., D.L. Diamond, C.D. Corley, A. Rasmussen, M.G. Katze, and K.M. Waters. 2012. "Topological Analysis of Protein Co-Abundance Networks Identifies Novel Host Targets Important for HCV Infection and Pathogenesis." BMC Systems Biology 6, no. 1:28. PNWD-SA-9359. doi:10.1186/1752-0509-6-28
• Schrimpe-Rutledge AC, G Fontes, MA Gritsenko, AD Norbeck, DJ Anderson, KM Waters, JN Adkins, RD Smith, V Poitout, and TO Metz.  2012.  Discovery of novel glucose-regulated proteins in isolated human pancreatic islets using LC-MS/MS-based proteomics.  Journal of Proteome Research, 11(7):3520-32. PMCID: PMC3391329.
• Shorey L., D.J. Castro, W.M. Baird, L.K. Siddens, C.V. Lohr, M.M. Matzke, and K.M. Waters, et al. 2012. "Transplacental Carcinogenesis with Dibenzo[def,p]chrysene (DBC): Timing of Maternal Exposures Determines Target Tissue Response in Offspring." Cancer Letters 317, no. 1:49-55. PNWD-SA-9570. doi:10.1016/j.canlet.2011.11.010
• Siddens L.K., A.J. Larkin, S.K. Krueger, C.A. Bradfield, K.M. Waters, S.C. Tilton, and C. Pereira, et al. 2012. "Polycyclic Aromatic Hydrocarbons as Skin Carcinogens: Comparison of Benzo[a]pyrene, Dibenzo[def,p]chrysene and Three Environmental Mixtures in the FVB/N Mouse." Toxicology and Applied Pharmacology 264, no. 3:377-386. PNWD-SA-9832. doi:10.1016/j.taap.2012.08.014
• Tal T., J. Franzosa, S.C. Tilton, K.A. Philbrick, U.T. Iwaniec, U.T. Iwaniec, and R.T. Turner, et al. 2012. "MicroRNAs Control Neurobehavioral Development and Function in Zebrafish." FASEB Journal 26, no. 4:1452-1461. PNWD-SA-9473. doi:10.1096/fj.11-194464
• Thomas S.N., K.M. Waters, W.F. Morgan, A. Yang, and J.E. Baulch. 2012. "Quantitative Proteomic Analysis of Mitochondrial Proteins Reveals Pro-Survival Mechanisms in the Perpetuation of Radiation-Induced Genomic Instability." Free Radical Biology & Medicine 53, no. 3:618-628. PNNL-SA-86050. doi:10.1016/j.freeradbiomed.2012.03.025
• Thrall B.D., K.R. Minard, J.G. Teeguarden, and K.M. Waters. 2012. Multiscale Toxicology - Building the Next Generation Tools for Toxicology. PNNL-21916. Richland, WA: Pacific Northwest National Laboratory. Multiscale Toxicology - Building the Next Generation Tools for Toxicology
• Tilton S.C., T. Tal, S.M. Scroggins, J. Franzosa, E.S. Peterson, R. Tanguay, and K.M. Waters. 2012. "Bioinformatics Resource Manager v2.3: An Integrated Software Environment for Systems Biology with microRNA and Cross-species Analysis Tools." BMC Bioinformatics 13:Article No. 311. PNWD-SA-9777. doi:10.1186/1471-2105-13-311
• Varnum S.M., D.L. Springer, M.E. Chaffee, K.A. Lien, B.M. Webb-Robertson, K.M. Waters, and C.A. Sacksteder. 2012. "The Effects of Low Dose Irradiation on Inflammatory Response Proteins in a 3D Reconstituted Human Skin Tissue Model." Radiation Research 178, no. 6:591-599. PNNL-SA-86146. doi:10.1667/RR2976.1
• Waters K.M., D.L. Stenoien, M.B. Sowa, C.H. Freiin Von Neubeck, W.B. Chrisler, R. Tan, and R.L. Sontag, et al. 2012. "Annexin A2 Modulates Radiation-Sensitive Transcriptional Programming and Cell Fate." Radiation Research 179, no. 1:56-61. PNNL-SA-84443. doi:10.1667/RR3056.1
• Waters K.M., T. Liu, R.D. Quesenberry, A.R. Willse, S. Bandyopadhyay, L.E. Kathmann, and T.J. Weber, et al. 2012. "Network Analysis of Epidermal Growth Factor Signaling using Integrated Genomic, Proteomic and Phosphorylation Data." PLoS One 7, no. 3:Article No. e34515. PNNL-SA-85737. doi:10.1371/journal.pone.0034515
• Yang F., K.M. Waters, B.M. Webb-Robertson, M.B. Sowa, C.H. Freiin von Neubeck, J.T. Aldrich, and L.M. Markillie, et al. 2012. "Quantitative Phosphoproteomics Identifies Filaggrin and other Targets of Ionizing Radiation in a Human Skin Model." Experimental Dermatology 21, no. 5:352-357. PNNL-SA-79030. doi:10.1111/j.1600-0625.2012.01470.x

2011

• Ahring B.K., N.S. Baliga, J.R. Frederickson, S. Kaplan, H.B. Pakrasi, J.G. Pounds, and I. shah, et al. 2011. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP). PNNL-20717. Richland, WA: Pacific Northwest National Laboratory. Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)
• Li C., A. Bankhead, A.J. Eisfeld, Y. Hatta, S. Jeng, J.H. Chang, and L.D. Aicher, et al. 2011. "Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus." Journal of Virology 85, no. 21:10955-10967. PNWD-SA-9325.
• Matzke M.M., K.M. Waters, T.O. Metz, J.M. Jacobs, A. Sims, R. Baric, and J.G. Pounds, et al. 2011. "Improved Quality Control Processing of Peptide-centric LC-MS Proteomics Data." Bioinformatics 27, no. 20:2866-2872. PNNL-SA-76540.
• McDermott J.E., H. Shankaran, A.J. Eisfeld, S. Belisle, G. Neumann, C. Li, and S.K. Mcweeney, et al. 2011. "Conserved Host Response to Highly Pathogenic Avian Influenza Virus Infection in Human Cell Culture, Mouse and Macaque Model Systems." BMC Systems Biology 5:Article No. 190. PNWD-SA-9377. doi:10.1186/1752-0509-5-190
• McDermott J.E., M.N. Archuleta, B.D. Thrall, J.N. Adkins, and K.M. Waters. 2011. "Controlling the Response: Predictive Modeling of a Highly Central, Pathogen-Targeted Core Response Module in Macrophage Activation." PLoS One 6, no. 2:e14673. PNWD-SA-9011. doi:10.1371/journal.pone.0014673
• Rasmussen A., D.L. Diamond, J.E. McDermott, X. Gao, T.O. Metz, M.M. Matzke, and V. Carter, et al. 2011. "Systems Virology Identifies a Mitochondrial Fatty Acid Oxidation Enyzme, Dodecenoyl Coenzyme A Delta Isomerase, Required for Hepatitis C Virus Replication and Likely Pathogenesis." Journal of Virology 85, no. 22:11646-11654. PNWD-SA-9324. doi:10.1128/JVI.05605-11
• Teeguarden J.G., B.M. Webb-Robertson, K.M. Waters, A. Murray, E. Kisin, S.M. Varnum, and J.M. Jacobs, et al. 2011. "Comparative Proteomics and Pulmonary Toxicity of Instilled Single Walled Carbon Nanotubes, Crocidolite Asbestos and Ultrafine Carbon Black in Mice." Toxicological Sciences 120, no. 1:123-135. PNNL-SA-74369. doi:10.1093/toxsci/kfq363
• Waters K.M., J.M. Jacobs, M.A. Gritsenko, and N.J. Karin. 2011. "Regulation of gene expression and subcellular protein distribution in MLO-Y4 osteocytic cells by lysophosphatidic acid: Relevance to dendrite outgrowth." Bone 48, no. 6:1328-35. PNNL-SA-74808. doi:10.1016/j.bone.2011.02.020
• Webb-Robertson B.M., M.M. Matzke, J.M. Jacobs, J.G. Pounds, and K.M. Waters. 2011. "A Statistical Selection Strategy for Normalization Procedures in LC-MS Proteomics Experiments through Dataset Dependent Ranking of Normalization Scaling Factors." Proteomics 11, no. 24:4736-4741. PNNL-SA-78392. doi:10.1002/pmic.201100078

2010

• Bailey V.L., S.J. Fansler, S. Bandyopadhyay, J.L. Smith, K.M. Waters, and H. Bolton. 2010. "Direct Detection of Soil mRNAs using Targeted Microarrays for Genes Associated with Lignin Degradation." Soil Biology and Biochemistry 42, no. 10:1793-1799. PNNL-SA-63713. doi:10.1016/j.soilbio.2010.06.017
• Diamond D.L., A.J. Syder, J.M. Jacobs, C.M. Sorensen, K. Walters, S. Proll, and J.E. McDermott, et al. 2010. "Temporal Proteome and Lipidome Profiles Reveal HCV-Associated Reprogramming of Hepatocellular Metabolism and Bioenergetics." PLoS Pathogens 6, no. 1:Article No. e1000719. PNWD-SA-8678. doi:10.1371/journal.ppat.1000719
• Webb-Robertson B.M., L.A. McCue, K.M. Waters, M.M. Matzke, J.M. Jacobs, T.O. Metz, and S.M. Varnum, et al. 2010. "Combined Statistical Analyses of Peptide Intensities and Peptide Occurrences Improves Identification of Significant Peptides from MS-based Proteomics Data." Journal of Proteome Research 9, no. 11:5748-5756. PNNL-SA-72886.
• Yang F., K.M. Waters, J.H. Miller, M.A. Gritsenko, R. Zhao, X. Du, and E.A. Livesay, et al. 2010. "Phosphoproteomics profiling of human skin fibroblast cells reveals pathways and proteins affected by low doses of ionizing radiation." PLoS One 5, no. 11:e14152. PNNL-SA-73768. doi:10.1371/journal.pone.0014152

2009

• Cannon W.R., B.M. Webb-Robertson, A.R. Willse, M. Singhal, L.A. McCue, J.E. McDermott, and R.C. Taylor, et al. 2009. "An Integrative Computational Framework for Hypotheses-Driven Systems Biology Research in Proteomics and Genomics." In Computational and Systems Biology: Methods and Applications. 63-85. Trivandrum:Research Signpost. PNNL-SA-57999.
• Castro D.J., C.V. Lohr, K.A. Fischer, K.M. Waters, B.M. Webb-Robertson, R.H. Dashwood, and G.S. Bailey, et al. 2009. "Identifying Efficacious Approaches to Chemoprevention with chlorophyllin, purified chlorophylls and freeze-dried spinach in a Mouse Model of Transplacental Carcinogenesis." Carcinogenesis 30, no. 2:315-320. PNNL-SA-60493.
• Waters K.M., L.M. Masiello, R.C. Zangar, B.J. Tarasevich, N.J. Karin, R.D. Quesenberry, and S. Bandyopadhyay, et al. 2009. "Macrophage Responses to Silica Nanoparticles are Highly Conserved Across Particle Sizes." Toxicological Sciences 107, no. 2:553-569. PNNL-SA-62659.
• Waters K.M., R. Tan, L.K. Opresko, R.D. Quesenberry, S. Bandyopadhyay, W.B. Chrisler, and T.J. Weber. 2009. "Cellular Dichotomy Between Anchorage-Independent Growth Responses to bFGF and TA Reflects Molecular Switch in Commitment to Carcinogenesis." Molecular Carcinogenesis 48, no. 11:1059-1069. PNNL-SA-57090.

2008

• Ding S., Y. Wang, J.M. Jacobs, W. Qian, F. Yang, A.V. Tolmachev, and X. Du, et al. 2008. "Quantitative Phosphoproteome Analysis of Lysophosphatidic Acid Induced Chemotaxis applying Dual-step ¹8O Labeling Coupled with Immobilized Metal-ion Affinity Chromatography." Journal of Proteome Research 7, no. 10:4215-24. PNNL-SA-52241. doi:10.1021/pr7007785
• Jacobs J.M., K.M. Waters, L.E. Kathmann, D.G. Camp, H.S. Wiley, R.D. Smith, and B.D. Thrall. 2008. "The Mammary Epithelial Cell Secretome and its Regulation by Signal Transduction Pathways." Journal of Proteome Research 7, no. 2:558-569. PNNL-SA-56310. doi:10.1021/pr0704377
• Rickard D.J., U.T. Iwaniec, U.T. Iwaniec, G. Evans, T.E. Hefferan, T.E. Hefferan, and J.C. Hunter, et al. 2008. "Bone growth and turnover in progesterone receptor knockout mice." Endocrinology 149, no. 5:2383-2390. PNNL-SA-57031. doi:10.1210/en.2007-1247
• Rogers S., M. Girolami, M. Girolami, W. Kolch, K.M. Waters, T. Liu, and B.D. Thrall, et al. 2008. "Investigating the Correspondence Between Transcriptomic and Proteomic Expression Profiles Using Coupled Cluster Models." Bioinformatics 24, no. 24:2894-2900. PNNL-SA-61286. doi:10.1093/bioinformatics/btn553
• Shah A.R., M. Singhal, T.D. Gibson, C. Sivaramakrishnan, K.M. Waters, and I. Gorton. 2008. "An extensible, scalable architecture for managing bioinformatics data and analysis." In IEEE 4th International Conference on e-Science, December 7-12, 2008, Indianapolis, Indiana, 190-197. Los Alamitos, California:IEEE Computer Society. PNWD-SA-8283. doi:10.1109/eScience.2008.69
• Webb-Robertson B.M., W.R. Cannon, C.S. Oehmen, A.R. Shah, V. Gurumoorthi, M.S. Lipton, and K.M. Waters. 2008. "A Support Vector Machine model for the prediction of proteotypic peptides for accurate mass and time proteomics." Bioinformatics 24, no. 13:1503-1509. PNNL-SA-60074. doi:10.1093/bioinformatics/btn218

2007

• Shah A.R., M. Singhal, K.R. Klicker, E.G. Stephan, H.S. Wiley, and K.M. Waters. 2007. "Enabling high-throughput data management systems biology: The Bioinformatics Resource Manager." Bioinformatics 23, no. 7:906-909. PNNL-SA-49327. doi:10.1093/bioinformatics/btm031
• Waters K.M., R. Tan, D.C. Genetos, S. Verma, C.E. Yellowley, and N.J. Karin. 2007. "DNA microarray analysis reveals a role for lysophosphatidic acid in the regulation of anti-inflammatory genes in MC3T3-E1 cells." Bone 41, no. 5:833-841. PNNL-SA-55566. doi:10.1016/j.bone.2007.06.029

2006

• Waters K.M., J.G. Pounds, and B.D. Thrall. 2006. "Data Merging for Integrated Microarray and Proteomic Analysis." Briefings in Functional Genomics and Proteomics 5, no. 4:261-272. PNNL-SA-47947. doi:10.1093/bfgp/ell019
• Waters K.M., M. Singhal, B.M. Webb-Robertson, E.G. Stephan, and J.M. Gephart. 2006. "Breaking the High-Throughput Bottleneck: New tools help biologists integrate complex datasets." Scientific Computing 23, no. 4:22-26. PNNL-SA-48217.

2002

• Rickard, DJ, KM Waters, TJ Ruesink, S Khosla, JA Katzenellenbogen, BS Katzenellenbogen, BL Riggs, and TC Spelsberg. 2002. Estrogen receptor isoform-specific induction of progesterone receptors in human osteoblasts. Journal of Bone and Mineral Research, 17, 580-592.

2001

• Waters, KM, S Safe, and KW Gaido. 2001. Differential gene expression in response to methoxychlor and estradiol through ERa, ERb and AR in reproductive tissues of female mice. Toxicological Sciences, 63, 47-56.
• Waters, KM, DJ Rickard, BL Riggs, S Khosla, JA Katzenellenbogen, BJ Katzenellenbogen, JT Moore and TC Spelsberg. 2001.  Estrogen regulation of human osteoblast function is determined by the stage of differentiation and the estrogen receptor isoform. Journal of Cellular Biochemistry, 83, 448-462. 
• Spelsberg, TC, M Subramaniam, KM Waters, TE Hefferan, DJ Rickard, and GG Reinholz. 2001. “A TGF-b/estrogen-inducible early gene (TIEG): A candidate tumor suppressor or cell cycle regulator?” Hormonal Carcinogenesis III, Eds. Li, J.J., Dahling, J.R., and Li, S.A., Springer-Verlag, New York, pp. 250-260.

2000

• Robinson, JA, KM Waters, RT Turner, and TC Spelsberg.  2000.  Direct action of naturally occurring estrogen metabolites on human osteoblastic cells. Journal of Bone and Mineral Research, 15, 499-506.
• Waters, KM, DJ Rickard, JB Gebhart, M Subramaniam, S Khosla, BL Riggs, J Moore, and TC Spelsberg.  2000.  Potential roles of estrogen receptor-alpha and –beta in the regulation of human osteoblast functions and gene expression.  The Menopause at the Millennium, T. Aso, T. Yanaihara & S. Fujimoto (Eds), Parthenon Publishing Group, New York, pp. 303-313. 
• Hefferan, TE, GG Reinholz, KM Waters, M Subramaniam, and TC Spelsberg. 2000. TGF-b inducible early gene (TIEG) overexpression mimics TGF-b action in human osteoblast cells. Journal of Biological Chemistry, 275, 20255-20259.

1999

• Waters, KM and TC Spelsberg. 1999.  Gonadal Steroids and Receptors. Primer on the Metabolic Bone Diseases and Disorders of Mineral Metabolism, 4^th Edition, M.J. Favus (Ed), Lippincott, Williams & Wilkins, pp 104-110.

1998

• Tau, KE, TE Hefferan, KM Waters, JA Robinson, M Subramaniam, BL Riggs, and TC Spelsberg. 1998. Estrogen regulation of a transforming growth factor-b inducible early gene that inhibits deoxyribonucleic acid synthesis in human osteoblasts. Endocrinology 139, 1346-1353.

1997

• Miller, CW, KM Waters, and JM Ntambi. 1997. Regulation of hepatic stearoyl-CoA desaturase gene 1 by vitamin A. Biochemical and Biophysical Research Communications, 231, 206-2104. 
• Waters, KM, CW Miller, and JM Ntambi. 1997. Localization of a negative thyroid hormone-response region in hepatic stearoyl-CoA desaturase gene 1. Biochemical and Biophysical Research Communications, 233, 838-843.
• Waters, KM, CW Miller, and JM Ntambi. 1997. Localization of a polyunsaturated fatty acid response region in stearoyl-CoA desaturase gene 1. Biochimica Biophysica Acta, 1349, 33-42.

1996

• Waters, KM and JM Ntambi. 1996. Polyunsaturated fatty acids inhibit hepatic stearoyl-CoA desaturase 1 gene in diabetic mice. Lipids, 31, S33-36.

1994

• Waters, KM and JM Ntambi. 1994. Insulin and dietary fructose induce stearoyl-CoA desaturase 1 gene expression in liver of diabetic mice. Journal of Biological Chemistry, 269(44), 27773-27777.